HIV/AIDS has become a serious global health hazard at a dimension unprecedented by any other infection. Human Immunodeficiency Virus type-1 (HIV-1) exhibits extremely high degree of variation at genetic level (Leitner et al., 2005). Based on the genetic homology, HIV-1 is classified into 9 distinct and primary genetic subtypes designated A through J (with the exception of E and I which are recombinants). Distribution of the viral subtypes across the globe is non-uniform. Additionally, epidemic outbreaks due to recombinant forms of the viruses are also becoming a serious problem in several geographical regions.
In addition to the above mentioned primary viral subtypes, a large number of recombinant viruses have been identified globally. Recombinant viruses arise when a genetic exchange takes place between two or more different viral strains generating a novel recombinant form (Najera et al., 2002). Depending on the epidemiologic incidence, recombinant viruses are of two types. First, circulating recombinant forms (CRF) are strains that have established successful infection in a geographical region or population and been characterized at the molecular level. The A/E virus of Thailand is one such recombinant virus. Second, the unique recombinant forms (URF), viruses that have been isolated from limited number of subjects and not adequately characterized at the molecular level. The incidence of global viral infections due to both the recombinant forms is on the rise at an alarmingly exponential rate. The total numbers of molecularly characterized CRFs has increased to 34 presently from 8 during the past 2-3 years. On the other hand, a large number of URFs are being identified on a regular basis. Generation and expansion of the recombinant viruses may throw serious challenges at disease intervention strategies like vaccine development and drug therapy (Najera et al., 2002; Lal et al., 2005; Peeters, 2000). It is therefore important to develop simple and inexpensive diagnostic strategies to detect recombinant viruses on a priority basis.
The objective of the present invention is to develop a novel and innovative strategy to detect primary subtypes and recombinant strains of HIV, preferably HIV-1. The same strategy is useful in assaying other types of viruses, bacteria, fungi, protozoa and parasites.
The assay is applicable to any kind of nucleic acids isolated from any kind of biological source including RNA and DNA without amplification.